6NXJ

Flavin Transferase ApbE from Vibrio cholerae, H257G mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Conserved residue His-257 ofVibrio choleraeflavin transferase ApbE plays a critical role in substrate binding and catalysis.

Fang, X.Osipiuk, J.Chakravarthy, S.Yuan, M.Menzer, W.M.Nissen, D.Liang, P.Raba, D.A.Tuz, K.Howard, A.J.Joachimiak, A.Minh, D.D.L.Juarez, O.

(2019) J Biol Chem 294: 13800-13810

  • DOI: https://doi.org/10.1074/jbc.RA119.008261
  • Primary Citation of Related Structures:  
    6NXI, 6NXJ

  • PubMed Abstract: 

    The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased K m values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the p K a of the catalytic residue (p K ES1 ) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 Å resolutions, revealing that His-257 is located in the catalytic site and that the substitution does not produce major conformational changes. We propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.


  • Organizational Affiliation

    Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD:protein FMN transferase
A, B
328Vibrio choleraeMutation(s): 1 
Gene Names: apbEC9J66_08705EN12_11145ERS013140_01021ERS013173_02114ERS013193_02472ERS013199_02400ERS013202_01888
EC: 2.7.1.180
UniProt
Find proteins for A5F5Y3 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Explore A5F5Y3 
Go to UniProtKB:  A5F5Y3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5F5Y3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.161α = 90
b = 71.922β = 93.29
c = 104.569γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description